Magnetic Ti3C2 MXene Nanosheets Prepared for Enrichment of Phosphopeptides

Application and mechanism of Co3O4/Co(OH)2 heterojunctions as matrices for small molecules detection by MALDI-TOF MS

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a superior technique for detecting small molecules, owing to the strategic utilization of inorganic nanomaterial matrices. Despite the impressive capabilities of various novel matrices, the underlying interaction mechanisms between inorganic matrices and analytes remain largely unexplored. In this study, we synthesized Co3O4 nanocubes, Co(OH)2 nanosheets, Co3O4/Co(OH)2 heterojunctions, and Co3O4+Co(OH)2 composites via a facile one-pot method. Amino acids were selected as model analytes for performance evaluation. Notably, the Co3O4/Co(OH)2 heterojunctions significantly enhanced signal intensity and lowered detection limits to the parts-per-billion (ppb) level, outperforming Co3O4 nanocubes, Co(OH)2 nanosheets, and Co3O4+Co(OH)2 composites. The detection results for environmental pollutants, especially in solutions containing real samples, highlight the outstanding performance of the heterojunction material as a matrix. Further characterization indicates that the formation of the heterojunction enhances nanoparticle dispersion and promotes the separation of photogenerated electron-hole pairs. Consequently, more photogenerated charge carriers can be transferred to the target analytes, facilitating their charging ability and ultimately enhancing signal intensity in MALDI-TOF MS. These results clearly demonstrate that the enhanced photocatalytic performance directly drives the improvement of MALDI-TOF MS performance, excluding interference from other factors. Thus, this study successfully combines photocatalytic mechanisms with MALDI-TOF MS mechanisms, providing new insights into the enhancement of MALDI-TOF MS performance. Additionally, it offers a new detection method for environmental pollutants.

Design of Ce3+ ions functionalized magnetic black phosphorus nanosheets for highly efficient enrichment of phosphopeptides

BACKGROUND

The abnormal variation of phosphorylation can lead to many human diseases, such as Alzheimer's disease and cancer. Because of its high throughput and rapidity, mass spectrometry (MS)-based method has been widely used to characterize phosphopeptides/phosphoproteins in complex biological samples. However, the direct MS analysis for phosphopeptides is still a challenging task due to the complexity of biological samples and the signal suppression of abundant non-phosphopeptides. Therefore, an efficient enrichment platform for low-abundance phosphopeptide capture and detection is in great demand.

RESULTS

In this study, Ce3+ ions functionalized magnetic black phosphorus nanosheets were successfully synthesized and characterized. The prepared magnetic material had high surface area (185.80 m2 g-1), good hydrophilicity (12.15°), and magnetic property (33.38 emu g-1). The magnetic material provided abundant affinity sites for phosphopeptide enrichment through immobilized metal ion affinity chromatography (IMAC). By combining MS analysis, the method exhibited satisfactory performance, including high sensitivity (0.1 fmol), good selectivity (α-casein: β-casein: BSA = 1: 1: 5000), and high recovery (87.2 %). The method was applied to enrich and detect phosphopeptides in skimmed milk, human saliva, serum, and A549 cell lysate, proving its feasibility for phosphopeptide analysis. Additionally, the method provided the sequence motifs of the captured phosphopeptides and the biological functions of the phosphoproteins in A549 cell lysate.

SIGNIFICANCE

This work presented a facile analysis platform for phosphopeptides, including sample preparation, enrichment process, and MS detection. The analysis strategy was successfully adopted for capturing and analyzing phosphopeptides from stranded proteins and complex bio-samples. This work presents a novel approach for the design and construction of black phosphorus-based adsorbents in phosphoproteomics research.

Theoretical Calculations in Separation Science for Analytical Chemistry: Applications and Insights

Separation and enrichment are critical steps in analytical detection, necessitating advanced materials with high selectivity and adsorption capacity for target compounds. In order to improve separation efficiency and selectivity, computational simulation could elucidate interaction mechanisms and analyze potential adsorption/desorption processes, providing a theoretical foundation for the optimization and design of separation materials. Recently, computational simulation has become an indispensable and crucial mean in separation science for analytical chemistry. Using various simulation software, researchers could investigate the structures, properties, and performance of separation materials at multiple levels and scales. In this review, we summarize the applications of computational simulations in the field of separation science, focusing on the separation of polar molecules, geometric isomers, enantiomer compounds, and post-translationally modified peptides. These calculation methods include quantum chemistry, molecular docking, molecular dynamics simulations, high-throughput screening, and machine learning. Finally, we discuss the current challenges and potential breakthroughs in computational simulation, aiming to offer valuable insights for researchers dedicated to computational simulation, material development, and separation applications.

Profiling the differential phosphoproteome between breast milk and infant formula through a titanium (IV)-immobilized magnetic nanoplatform

Breast milk (BM) fulfills the nutritional needs of infants and sets the standard for infant formula (IF). However, profiling the differential phosphoproteome between BM and IF remains unclear. Herein, a titanium (IV) (Ti4+)-immobilized magnetic nanoplatform (Fe3O4@GO@PDA-Ti4+) was constructed by self-assembly polymerization of dopamine on magnetic graphene oxide, followed by immobilizing Ti4+ through chelation for phosphopeptide enrichment. Fe3O4@GO@PDA-Ti4+ possessed outstanding selectivity (1/1000, a molar ratio of β-casein digests to bovine serum albumin digests) and favorable sensitivity (2.5 fmol/μL), along with rapid magnetic separation. Excellent phosphopeptide capture efficiencies were obtained for BM and IF using Fe3O4@GO@PDA-Ti4+ as an adsorbent coupled with liquid chromatography-mass spectrometry/mass spectrometry. There were 191 and 239 phosphopeptides found in BM and IF, respectively, with 36 phosphoproteins identified in both. However, BM and IF shared only 17 phosphopeptides and 4 phosphoproteins. The variation in the phosphoproteome between BM and IF provides valuable insights into the optimization of IF humanization.

In Situ MXene-Controlled Synthesis of Polycrystalline TiO2 for Highly Efficient Enrichment of Phosphopeptides

Phosphopeptide enrichment methods based on commercial TiO2 suffer from difficulties in regulating intermolecular interactions, resulting in low coverage rate and the loss of information on multiphosphorylation sites, thereby limiting comprehensive phosphoproteomic analysis. In this work, MXene Ti3C2Tx was incorporated into the design of enrichment materials, with its surface structure functionalized and regulated to address the low elution efficiency of TiO2 for multiphosphorylated peptides. Upon oxidation treatment, the Ti3C2Tx material formed numerous uniformly distributed TiO2 nanoparticles on the surface of Ti3C2Tx-O, providing abundant affinity sites (Ti-O) for selective phosphopeptide enrichment. The polycrystalline structure and rich oxygen vacancies of the material effectively regulated its binding affinity with phosphate groups, achieving simultaneous high-efficiency enrichment of both monophosphorylated and multiphosphorylated peptides. Its performance was significantly superior to that of commercial TiO2 and IMAC materials. This study presents great promise for the practical application of comprehensive phosphoproteomic analysis in the future and broadens the application of MXene in the biological field.

Advanced functional materials as reliable tools for capturing food-derived peptides to optimize the peptidomics pre-treatment enrichment workflow

Peptidomics strategies with high throughput, sensitivity, and reproducibility are key tools for comprehensively analyzing peptide composition and potential functional activities in foods. Nevertheless, complex signal interference, limited ionization efficiency, and low abundance have impeded food-derived peptides' progress in food detection and analysis. As a result, novel functional materials have been born at the right moment that could eliminate interference and perform efficient enrichment. Of note, few studies have focused on developing peptide enrichment materials for food sample analysis. This work summarizes the development of endogenous peptide, phosphopeptide, and glycopeptide enrichment utilizing materials that have been employed extensively recently: organic framework materials, carbon-based nanomaterials, bio-based materials, magnetic materials, and molecularly imprinted polymers. It focuses on the limitations, potential solutions, and future prospects for application in food peptidomics of various advanced functional materials. The size-exclusion effect of adjustable aperture and the modification of magnetic material enhanced the sensitivity and selectivity of endogenous peptide enrichment and aided in streamlining the enrichment process and cutting down on enrichment time. Not only that, the immobilization of metal ions such as Ti4+ and Nb5+ enhanced the capture of phosphopeptides, and the introduction of hydrophilic groups such as arginine, L-cysteine, and glutathione into bio-based materials effectively optimized the hydrophilic enrichment of glycopeptides. Although a portion of the carefully constructed functional materials currently only exhibit promising applications in the field of peptide enrichment for analytical chemistry, there is reason to believe that they will further advance the field of food peptidomics through improved pre-treatment steps.

Aptamer-Functionalized Magnetic Ti3C2 Based Nanoplatform for Simultaneous Enrichment and Detection of Exosomes

Exosomes are nanovesicles secreted by cells, which play a crucial role in various pathological processes. Exosomes have shown great promise as tumor biomarkers because of the abundant secretion during tumor formation. The development of a convenient, efficient, and cost-effective method for simultaneously enriching and detecting exosomes is of utmost importance for both basic research and clinical applications. In this study, an aptamer-functionalized magnetic Ti3C2 composite material (Fe3O4@Ti3C2@PEI@DSP@aptamer@FAM-ssDNA) is prepared for the simultaneous enrichment and detection of exosomes. CD63 aptamers are utilized to recognize and capture the exosomes, followed by magnetic separation. The exosomes are then released by cleaving the disulfide bonds of DSP. Compared to traditional methods, Fe3O4@Ti3C2@PEI@DSP@aptamer@FAM-ssDNA exhibited superior efficiency in enriching exosomes while preserving their structural and functional integrity. Detection of exosome concentration is achieved through the fluorescence quenching of Ti3C2 and the competitive binding between the exosomes and a fluorescently labeled probe. This method exhibited a low detection limit of 4.21 × 104 particles mL-1, a number that is comparable to the state-of-the-art method in the detection of exosomes. The present study demonstrates a method of simultaneous enrichment and detection of exosomes with a high sensitivity, accuracy, specificity, and cost-effectiveness providing significant potential for clinical research and diagnosis.

Organic-Inorganic Interfacial Dipole Induced by Energy Level Alignment for Efficient Photocatalytic Sterilization

Photocatalytic molecules are considered to be one of the most promising substitutions of antibiotics against multidrug-resistant bacterial infections. However, the strong excitonic effect greatly restricts their efficiency in antibacterial performance. Inspired by the interfacial dipole effect, a Ti3C2 MXene modified photocatalytic molecule (MTTTPyB) is designed and synthesized to enhance the yield of photogenerated carriers under light irradiation. The alignment of the energy level between Ti3C2 and MTTTPyB results in the formation of an interfacial dipole, which can provide an impetus for the separation of carriers. Under the role of a dipole electric field, these photogenerated electrons can rapidly migrate to the side of Ti3C2 for improving the separation efficiency of photogenerated electrons and holes. Thus, more electrons can be utilized to produce reactive oxygen species (ROS) under light irradiation. As a result, over 97.04% killing efficiency can be reached for Staphylococcus aureus (S. aureus) when the concentration of MTTTPyB/Ti3C2 was 50 ppm under 660 nm irradiation for 15 min. A microneedle (MN) patch made from MTTTPyB/Ti3C2 was used to treat the subcutaneous bacterial infection. This design of an organic-inorganic interface provides an effective method to minimize the excitonic effect of molecules, further expanding the platform of inorganic/organic hybrid materials for efficient phototherapy.

Multimodal Affinity-Modulated Efficient Separation of Lysozyme with a Hierarchical MXene@MOF Hybrid Framework

The development of abiotic protein affinity adsorbents remains challenging for the accurate acquisition and analysis of specific protein species. Inspired by bacterial cell walls, a hierarchical hybrid framework is fabricated through the oriented growth of an Fe-based metal organic framework (MOF) on V2C MXene for the efficient separation of lysozyme (Lys). After directed evolution of adsorptive materials, the MXene@MOF composite rich in hydroxyl groups (termed as MX@MOF-DH) is found exerting exceptional affinity for Lys. Benefiting from hydrogen-bonding, coordination, and electrostatic interaction-mediated multimodal and multivalent affinity, MX@MOF-DH reveals rapid adsorption rate (5 min), superb enrichment factor (83.1), and favorable binding capacity (609.7 mg g-1), which outperforms other latest adsorbents. Moreover, femtomolar sensitivity is achieved even in the presence of high-abundant interfering proteins, as confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometer analysis. This work not only provides an efficient approach for selective enrichment of lysozyme but also paves an avenue to construct the protein affinity reagents for specific biological medicine and analysis applications.

Enrichment of Phosphopeptides Based on Zirconium Phthalocyanine-Modified Magnetic Nanoparticles

Highly selective extraction of phosphopeptides is necessary before mass spectrometry (MS) analysis. Herein, zirconium phthalocyanine-modified magnetic nanoparticles were prepared through a simple method. The Fe-O groups on Fe3O4 and the zirconium ions on phthalocyanine had a strong affinity for phosphopeptides based on immobilized metal ion affinity chromatography (IMAC). The enrichment platform exhibited low detection limit (0.01 fmol), high selectivity (α-/β-casein/bovine serum albumin, 1/1/5000), good reusability (10 circles), and recovery (91.1 ± 1.1%) toward phosphopeptides. Nonfat milk, human serum, saliva, and A549 cell lysate were employed as actual samples to assess the applicability of the enrichment protocol. Metallo-phthalocyanine will be a competitive compound for designing highly efficient adsorbents and offers a new approach to phosphopeptide analysis.

Preparation of high-efficiency titanium ion immobilized magnetic graphite nitride nanocomposite for phosphopeptide enrichment

BACKGROUND

Protein phosphorylation has been implicated in life processes including molecular interaction, protein structure transformation, and malignant disease. An in-depth study of protein phosphorylation may provide vital information for the discovery of early biomarkers. Mass spectrometry (MS)-based techniques have become an important method for phosphopeptide identification. Nevertheless, direct detection remains challenging because of the low ionization efficiency of phosphopeptides and serious interference from non-phosphopeptides. There is a great need for an efficient enrichment strategy to analyze protein phosphorylation prior to MS analysis.

RESULTS

In this study, a novel nanocomposite was prepared by introducing titanium ions into two-dimensional magnetic graphite nitride. The nanocomposite was combined with immobilized metal ion affinity chromatography (IMAC) and anion-exchange chromatography mechanisms for phosphoproteome research. The nanocomposite had the advantages of a large specific surface (412.9 m2 g-1), positive electricity (175.44 mV), and excellent magnetic property (35.7 emu g-1). Moreover, it presented satisfactory selectivity (α-casein:β-casein:bovine serum albumin = 1:1:5000), a low detection limit (0.02 fmol), great recyclability (10 cycles), and high recovery (92.8%). The nanocomposite demonstrated great practicability for phosphopeptides from non-fat milk, human serum, and saliva. Further, the nanocomposite was applied to enrich phosphopeptides from a more complicated specimen, A549 cell lysate. A total of 890 phosphopeptides mapping to 564 phosphoproteins were successfully detected with nano LC-MS.

SIGNIFICANCE

We successfully designed and developed an efficient analysis platform for phosphopeptides, which includes protein digestion, phosphopeptide enrichment, and MS detection. The MS-based enrichment platform was further used to analyze phosphopeptides from complicated bio-samples. This work paves the way for the design and preparation of graphite nitride-based IMAC materials for phosphoproteome analysis.

Effective Enrichment of Phosphopeptides Using Magnetic Polyoxometalate-Based Metal-Organic Frameworks

In this study, magnetic polyoxometalate-based metal-organic frameworks (Fe3O4-POMOFs) were designed and applied to the enrichment of phosphopeptides. Thanks to the abundant metal oxide and metal ion sites, the material had a strong affinity for phosphopeptides. Simultaneously, the high amount of amino and guanidyl groups provided hydrophilicity and positive charge for phosphopeptide capture. By coupling with MS detection, the established platform possessed good reusability, high sensitivity (0.01 fmol), and high selectivity (α-casein/β-casein/bovine serum albumin = 1:1:5000). Furthermore, the method was successfully used for the detection of phosphopeptides in nonfat milk, human serum, saliva, and A549 cell lysate, showing great potential for practical application.

Magnetic resin composites for the enrichment of proteins, peptides and phosphopeptides

There is growing interest in the development of materials for enriching proteins and phosphoproteins from complex sample matrices for mass spectrometric analysis. Herein, we designed and synthesized two types of magnetic resin composites, i.e., MTS9200@Fe3O4 and FPA90CL@Fe3O4, and assessed their applications as adsorbents for enriching proteins, peptides and phosphopeptides. With the combination of Fe3+-IMAC interaction (MTS9200) or electrostatic attraction (FPA90CL) of resins and the adsorption of Fe3O4, the prepared composites exhibited higher capacities for adsorbing a protein (bovine serum albumin, at 195.71 and 135.03 mg g-1 for MTS9200@Fe3O4 and FPA90CL@Fe3O4, respectively) than MTS9200, FPA90CL and Fe3O4. In addition, due to the contributions of the hydrophobic skeleton of resins and Fe3O4, the magnetic resin composites allowed for efficient enrichment of peptides. Moreover, through Fe3+-IMAC interaction or electrostatic attraction of resins and Fe-O MOAC interaction of Fe3O4 with phosphate groups, phosphopeptides could also be captured. Furthermore, we employed the prepared composites for enriching proteins and phosphopeptides from human serum, where 466 and 506 proteins, and 434 and 356 phosphorylation sites, were detected from human serum after being processed with FPA90CL@Fe3O4 and MTS9200@Fe3O4, respectively. Together, our work revealed the great potential of magnetic resin composites as enrichment materials for proteomics and phosphoproteomics analysis.